Alignments for a candidate for aroB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Phaeobacter inhibens BS107

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF1393 PGA1_c14100 3-dehydroquinate synthase AroB

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__Phaeo:GFF1393
          Length = 375

 Score =  279 bits (713), Expect = 1e-79
 Identities = 164/363 (45%), Positives = 216/363 (59%), Gaps = 9/363 (2%)

Query: 81  VEVDLGTRSYPIYIGAGLL-DQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNP 139
           V V LG R+Y + IG  LL D    L   +   +V V+T+ TVA  +L+   + L     
Sbjct: 10  VHVALGERAYDVVIGPDLLADAGARLAPMLRRPKVAVLTDETVAAHHLEGLRAGLASAG- 68

Query: 140 NVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLR 199
            + ++++ LP GE  K      +  +  +E +++R    +A GGGVIGD+ G+AAA   R
Sbjct: 69  -IEMDALALPPGESTKAWPQFSRAVEWLLEQKVERGDIVIAFGGGVIGDLAGFAAAVLRR 127

Query: 200 GVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELAS 259
           GV F+QIPT+++AQVDSSVGGKTGIN P GKN+IGAF+QP  VL DT  L TL  R+  +
Sbjct: 128 GVRFVQIPTSLLAQVDSSVGGKTGINAPQGKNLIGAFHQPSLVLADTALLGTLTPRDFLA 187

Query: 260 GLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVR 319
           G  EV+KYGL+ DAEFFEW E   P L A D  A   A+ RS + KAD+V +DE E G R
Sbjct: 188 GYGEVVKYGLLGDAEFFEWLEAQGPALAAGDMAARVEAVTRSVQMKADIVVRDETEQGDR 247

Query: 320 ATLNLGHTFGHAVETGVGYG-QWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQ 378
           A LNLGHTF HA+E   GYG + LHGE VA G  +A ++S RLG        RV+  L+ 
Sbjct: 248 ALLNLGHTFCHALEAATGYGDRLLHGEGVAIGCALAFELSARLGLCSQEDPSRVRAHLKA 307

Query: 379 AKLPTS----PPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDE 434
             + T     P E    E   ++M  DKKV DG+LR IL +G +G    TGD  Q A+ +
Sbjct: 308 MGMKTDLADIPGELPDAEALLALMGQDKKVVDGQLRFILARG-IGQAFVTGDVPQAAVLD 366

Query: 435 TLR 437
            LR
Sbjct: 367 VLR 369


Lambda     K      H
   0.318    0.133    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 357
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 442
Length of database: 375
Length adjustment: 31
Effective length of query: 411
Effective length of database: 344
Effective search space:   141384
Effective search space used:   141384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1393 PGA1_c14100 (3-dehydroquinate synthase AroB)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01357.hmm
# target sequence database:        /tmp/gapView.7879.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.9e-111  356.5   0.0   8.9e-111  356.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1393  PGA1_c14100 3-dehydroquinate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1393  PGA1_c14100 3-dehydroquinate synthase AroB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.3   0.0  8.9e-111  8.9e-111       1     341 [.      19     366 ..      19     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.3 bits;  conditional E-value: 8.9e-111
                          TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldq 74 
                                        y+v++g +ll+ + + la   ++ k+ v+tde+v++++ e l++ l+s+g+e++ l +p+ge++K + ++++ +++
  lcl|FitnessBrowser__Phaeo:GFF1393  19 YDVVIGPDLLADAGARLAPmlRRPKVAVLTDETVAAHHLEGLRAGLASAGIEMDALALPPGESTKAWPQFSRAVEW 94 
                                        7899*******99999999766699*************************************************** PP

                          TIGR01357  75 lleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaV 150
                                        lle+k+er ++++a+GGGv+gDlaGF+Aa+  RG+r+vq+PT+lla+vDssvGGKtgin p+gkNliGaf+qP++V
  lcl|FitnessBrowser__Phaeo:GFF1393  95 LLEQKVERGDIVIAFGGGVIGDLAGFAAAVLRRGVRFVQIPTSLLAQVDSSVGGKTGINAPQGKNLIGAFHQPSLV 170
                                        **************************************************************************** PP

                          TIGR01357 151 lidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesg 226
                                        l d+++l tl+ r + +G++Ev+K+gl+ dae+fe+le +  +l    +++a  e+++rs+++Ka++V +De+e+g
  lcl|FitnessBrowser__Phaeo:GFF1393 171 LADTALLGTLTPRDFLAGYGEVVKYGLLGDAEFFEWLEAQGPALAA-GDMAARVEAVTRSVQMKADIVVRDETEQG 245
                                        ***************************************9998776.5669999********************** PP

                          TIGR01357 227 lRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkk....k 296
                                         RalLN+GHt+ Ha+Ea+++y+  l HGe VaiG +++++ls +lgl+++e+ +r++a lk++g++t+l +     
  lcl|FitnessBrowser__Phaeo:GFF1393 246 DRALLNLGHTFCHALEAATGYGdrLLHGEGVAIGCALAFELSARLGLCSQEDPSRVRAHLKAMGMKTDLADipgeL 321
                                        *********************999**********************************************999987 PP

                          TIGR01357 297 lsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                         ++e+ll+ + +DKK  +++++++l++ iG+a+++ +v++ ++l+
  lcl|FitnessBrowser__Phaeo:GFF1393 322 PDAEALLALMGQDKKVVDGQLRFILARGIGQAFVTGDVPQAAVLD 366
                                        89********************************99999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (375 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.42
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis